chrX-8184147-A-G

Variant names:

• chrX-8184147-A-G
• rs2278935
• ENST00000649338.1:n.263-44188A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649338.1(ENSG00000285679):​n.263-44188A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 111,693 control chromosomes in the GnomAD database, including 5,203 homozygotes. There are 10,926 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (5203 hom., 10926 hem., cov: 24)
• Consequence: ENSG00000285679 ENST00000649338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 2 publications found

Genes affected

ENSG00000285679 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649338.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285679	ENST00000649338.1		n.263-44188A>G		intron	N/A
	ENSG00000285679	ENST00000659022.1		n.972-44188A>G		intron	N/A
	ENSG00000285679	ENST00000746118.1		n.326-44188A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 36586 AN: 111636 Hom.: 5206 Cov.: 24

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.320

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.328 AC: 36642 AN: 111693 Hom.: 5203 Cov.: 24 AF XY: 0.322 AC XY: 10926 AN XY: 33943

African (AFR) AF: 0.552 AC: 16931 AN: 30657

American (AMR) AF: 0.334 AC: 3536 AN: 10595

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 634 AN: 2640

East Asian (EAS) AF: 0.595 AC: 2093 AN: 3518

South Asian (SAS) AF: 0.272 AC: 743 AN: 2728

European-Finnish (FIN) AF: 0.199 AC: 1206 AN: 6069

Middle Eastern (MID) AF: 0.324 AC: 70 AN: 216

European-Non Finnish (NFE) AF: 0.205 AC: 10862 AN: 53071

Other (OTH) AF: 0.328 AC: 499 AN: 1523

Alfa AF: 0.263 Hom.: 20789

Bravo AF: 0.359

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.40
PhyloP100		-0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2278935; hg19: chrX-8152188;